Add back fully-qualified registry URIs

[ewels]

Nextflow v25.10 introduced a new config option docker.registryOverride. This allows folks to use their own mirrors of nf-core module containers.

We have had a workaround for a while now where all modules don't include their host and fall back to the default docker.registry that is set in the pipeline config, allowing people to configure mirrors with docker.registry. Now that we have docker.registryOverride this workaround is not needed.

It's better to have modules self-sufficient (not requiring a pipeline-level config attribute), so this PR goes back to how we used to do it with fully qualified URIs for all container attributes.

docker.registry should be ignored if a fully qualified URI is found (this already happens for Seqera Container URIs), so this should not be a breaking change. In the future, we can remove docker.registry from the pipeline config, but it's not required.

Non-standard containers

In doing this work, I uncovered a few modules that have non-standard containers. Thought I'd list here just in case any are worth following up.

nvcr.io/nvidia — 1 image(s), 12 module reference(s)

Module	Container
parabricks/applybqsr	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1
parabricks/dbsnp	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1
parabricks/deepvariant	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1
parabricks/fq2bam	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1
parabricks/fq2bammeth	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1
parabricks/genotypegvcf	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1
parabricks/haplotypecaller	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1
parabricks/indexgvcf	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1
parabricks/minimap2	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1
parabricks/mutectcaller	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1
parabricks/rnafq2bam	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1
parabricks/starfusion	nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1

ghcr.io/schapirolabor — 8 image(s), 8 module reference(s)

Module	Container
backsub	ghcr.io/schapirolabor/background_subtraction:v0.5.1
celesta	ghcr.io/schapirolabor/mcmicro-celesta:v0.0.2
imc2mc	ghcr.io/schapirolabor/imc2mc:0.0.3
mcstaging/imc2mc	ghcr.io/schapirolabor/imc2mc:0.0.2
mcstaging/macsima2mc	ghcr.io/schapirolabor/macsima2mc:v1.2.15
mcstaging/phenoimager2mc	ghcr.io/schapirolabor/phenoimager2mc:v0.2.2
molkartgarage/clahe	ghcr.io/schapirolabor/molkart-local:v0.1.1
phenoimager2mc	ghcr.io/schapirolabor/phenoimager2mc:v0.3.2

docker.io/google — 3 image(s), 7 module reference(s)

Module	Container
deepsomatic	docker.io/google/deepsomatic:1.7.0
deepvariant	docker.io/google/deepvariant:1.9.0
deepvariant/callvariants	docker.io/google/deepvariant:1.9.0
deepvariant/makeexamples	docker.io/google/deepvariant:1.9.0
deepvariant/postprocessvariants	docker.io/google/deepvariant:1.9.0
deepvariant/rundeepvariant	docker.io/google/deepvariant:1.10.0
deepvariant/vcfstatsreport	docker.io/google/deepvariant:1.10.0

docker.io/biocontainers — 3 image(s), 5 module reference(s)

Module	Container
diann	docker.io/biocontainers/diann:v1.8.1_cv1
diann/insilicolibrarygeneration	docker.io/biocontainers/diann:v1.8.1_cv1
ilastik/multicut	docker.io/biocontainers/ilastik:1.4.0_cv1
ilastik/pixelclassification	docker.io/biocontainers/ilastik:1.4.0_cv1
ncbitools/vecscreen	docker.io/biocontainers/ncbi-tools-bin:6.1.20170106-6-deb_cv2

docker.io/labsyspharm — 3 image(s), 3 module reference(s)

Module	Container
basicpy	docker.io/labsyspharm/basicpy-docker-mcmicro:1.2.0-patch5
coreograph	docker.io/labsyspharm/unetcoreograph:2.2.9
scimap/mcmicro	docker.io/labsyspharm/scimap:2.1.3

quay.io/khersameesh24 — 1 image(s), 3 module reference(s)

Module	Container
opt/flip	quay.io/khersameesh24/opt:v0.0.1
opt/stat	quay.io/khersameesh24/opt:v0.0.1
opt/track	quay.io/khersameesh24/opt:v0.0.1

docker.io/ncbi — 2 image(s), 2 module reference(s)

Module	Container
fcs/fcsadaptor	docker.io/ncbi/fcs-adaptor:0.5.0
fcs/fcsgx	docker.io/ncbi/fcs-gx:0.4.0

ghcr.io/marcelauliano — 1 image(s), 2 module reference(s)

Module	Container
mitohifi/findmitoreference	ghcr.io/marcelauliano/mitohifi:3.2.3
mitohifi/mitohifi	ghcr.io/marcelauliano/mitohifi:3.2.3

https://ftp.ncbi.nlm.nih.gov — 2 image(s), 2 module reference(s)

Module	Container
fcs/fcsadaptor	https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.5.0/fcs-adaptor.sif
fcs/fcsgx	https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.4.0/fcs-gx.sif

docker.io/clinicalgenomics — 1 image(s), 1 module reference(s)

Module	Container
cadd	docker.io/clinicalgenomics/cadd-with-scripts:1.7.3

docker.io/elembio — 1 image(s), 1 module reference(s)

Module	Container
bases2fastq	docker.io/elembio/bases2fastq:2.3.0

docker.io/felbecker — 1 image(s), 1 module reference(s)

Module	Container
learnmsa/align	docker.io/felbecker/learnmsa:2.0.14

docker.io/hkubal — 1 image(s), 1 module reference(s)

Module	Container
clair3	docker.io/hkubal/clair3:v2.0.0

docker.io/miguelib — 1 image(s), 1 module reference(s)

Module	Container
scimap/spatiallda	docker.io/miguelib/scimap:0.0.3

docker.io/teambraker — 1 image(s), 1 module reference(s)

Module	Container
braker3	docker.io/teambraker/braker3:v3.0.7.5

ghcr.io/nbisweden — 1 image(s), 1 module reference(s)

Module	Container
genescopefk	ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2

ghcr.io/scverse — 1 image(s), 1 module reference(s)

Module	Container
scvitools/solo	ghcr.io/scverse/scvi-tools:py3.12-cu12-1.3.3-

us.gcr.io/broad-dsde-methods — 1 image(s), 1 module reference(s)

Module	Container
cellbender/removebackground	us.gcr.io/broad-dsde-methods/cellbender:0.3.2

[ewels]

.github/workflows/lint.yml (Line: 125, Col: 7): Strategy for job 'nf-core-lint-modules' produced 1104 configurations which exceeds the maximum of 256 configurations

[maxulysse]

fine for me

[mashehu]